EMPIAR-12779 - Cryo-ET of D. melanogaster Nup358::VN/Nup358::VC cells [multiple data sets in MRC format]

EMPIAR-12779

Cryo-ET of D. melanogaster Nup358::VN/Nup358::VC cells [multiple data sets in MRC format]

Publication:

The small GTPase Ran defines Nuclear Pore Complex Asymmetry

Sachweh J, Börmel M, Klumpe S, Becker A, Taniguchi R, Kubańska MA, Pintschovius V, Kaindl E, Plitzko JM, Wilfling F, Beck M, Hampoelz B

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Related EMDB entry:

EMD-53740 EMD-53745 EMD-53751 EMD-53739 EMD-53746 EMD-53743 EMD-53744 EMD-53741 EMD-53747 EMD-53742

Deposited:

2025-05-14

Released:

2025-09-04

Last modified:

2025-09-04

Imageset size:

307.94 GB

Imageset DOI:

10.6019/EMPIAR-12779

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes

Image Sets

1. Tilt series of D. melanogaster Nup358::VN/Nup358::VC cells

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

111

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(2.414, 2.414)

Details:

Tilt series were frame-aligned in SerialEM during acquisition, mrc and mdoc files for the stacks are provided. The subfolder "alignment_files", contains alignment files (.xf) and tilt files (.tlt) that were generated by IMOD, CTF estimation from gctf are included as gctf.star files. The cleaned tilt fils lists images excluded from raw stacks.

Files:

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2. Filtered tomograms of D. melanogaster Nup358::VN/Nup358::VC cells

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

111

Image size:

(1024, 1024)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(9.656, 9.656)

Details:

Non-CTF corrected tomograms reconstructed at bin 4 and processed by SIRT-like filtering in IMOD are provided.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

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Citations

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He L, Bartesaghi A. (2026)

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Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

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Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)